[phenixbb] Excluding atoms from coordinate refinement ignored

Pavel Afonine pafonine at lbl.gov
Fri Dec 21 17:00:52 PST 2012

Hi Engin,

that's bad. Could you please send me inputs so I can reproduce this?


On 12/21/12 4:55 PM, Engin Özkan wrote:
> Hi Phenix developers,
> I have an issue using 1.8.1 (1168) with excluding atoms from 
> coordinate refinement. I have defined a certain residue to be excluded 
> from coordinate refinement, as can be seen in the .eff file produced 
> by this run.
>   refine {
>     strategy = *individual_sites individual_sites_real_space rigid_body \
>                *individual_adp group_adp *tls *occupancies 
> group_anomalous
>     sites {
>       individual = not (resseq 60 and resname PHE)
>       torsion_angles = not (resseq 60 and resname PHE)
>       rigid_body = None
> ...
> However, this gets ignored, and this residue and its NCS-related 
> brethren get moved into nondescript electron density on a symmetry 
> axis. This residue was just fine in an earlier version of Phenix, but 
> when I switched to 1.8.1, it started moving into this density. So, I 
> thought excluding it from xyz refinement, which is a dirty trick in my 
> opinion, would fix this problem. Not so.
> I have the feeling that this is due to rotamer corrections as part of 
> the torsion NCS implemented in 1.8.1 now. Sticking a zero occupancy 
> dummy atom in the density did prevent this residue from moving in. 
> Turning off torsion NCS also fixed it. By the way, I have "fix rotamer 
> sidechains" off, as I am yet to see it improve things (at medium or 
> low resolution).
> Thanks and happy holidays!
> Engin
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